Re: [gmx-users] gmx xpm2ps

"gmx xpm2ps -f hbmap.xpm - o hbplot.eps -rainbow red" -> "gmx xpm2ps -f hbmap.xpm -o hbplot.eps -rainbow red" You have a blanck space between the "-" and the "o". On Fri, Mar 31, 2017 at 5:52 PM Kulkarni R wrote: > Hi gromacs users, > > > After completing

Re: [gmx-users] The Berendsen thermostat does not generate the correct kinetic energy distribution.

I guess the best way to understand it is to read the original works: http://dx.doi.org/10.1063/1.448118 http://dx.doi.org/10.1063/1.2408420 And try to understand the differences between the two. Afterwards, you should be able to make a choice suitable for your case. Best, Diogo On Mon, Nov 28,

Re: [gmx-users] How to visualizing gro file in pymol

This can help you: http://manual.gromacs.org/programs/gmx-editconf.html Nevertheless, you can simply type: editconf -f structure.gro -o structure.pdb On Wed, Feb 3, 2016 at 10:34 AM anu chandra wrote: > Hello all, > > I just finished a short simulation of a membrane

Re: [gmx-users] How the topology file is created based on *.gro file?

If you still need to correct your numbering (for scripting porposes for example) you can convert your original.gro using editconf and in the final gro file will be corrected. On Wed, Feb 3, 2016 at 11:24 AM Dawid das wrote: > So it turns out that what is important is the

Re: [gmx-users] question

I am not sure but probably you only need to change the residue names in the pdb file. You should also be carefull with other bonded parameters (angles and dihedrals). Em qua, 13 de mai de 2015 às 04:56, Andrew Bostick andrew.bosti...@gmail.com escreveu: Dear Justin Since I want to consider

Re: [gmx-users] During mdrun my protein moves towards edges

You do not have a problem you only have the normal protein diffusion. Take a look in trjconv tool. http://manual.gromacs.org/programs/gmx-trjconv.html Option -center will be your best friend I guess. Diogo Vila-Viçosa Em seg, 11 de mai de 2015 às 10:14, Seera Suryanarayana paluso

Re: [gmx-users] Distance Restraints

you want is a distance restraints or an actual bond between the Zn and the S atoms (four I guess). Diogo Vila Viçosa Em qui, 7 de mai de 2015 às 18:58, Steve Seibold steve...@ymail.com escreveu: I have a two peptide system with my second chain B having as part of its topology file

Re: [gmx-users] Helicity

the average helicity of the peptide during the specified time. Thanks, sxn On Fri, Feb 6, 2015 at 3:11 PM, Diogo Vila Viçosa diogo.vic...@fc.ul.pt wrote: I Shivangi, There are several ways to calculate the average helicity. If you are using linux you can easily do

Re: [gmx-users] Helicity

you are using linux and my advice to you is: try to learn something about awk, sed, bash, etc... before you dive in into more complex things such as a MD simulation. Best regards, Diogo Vila Viçosa shivangi nangia shivangi.nan...@gmail.com escreveu no dia Fri Feb 06 2015 at 20:00:41: Hello